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MPHARM > Primary structure of proteins > Flashcards

Primary structure of proteins Flashcards

1
Q

DNA makes RNA which makes Proteins.
(extra reading- Instant notes: Biochemistry)

A
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2
Q

Name 6 functions of proteins

  • Provide examples of proteins for each function
A

Catalysis
Enzymes:
Proteases – breaks proteins
ATPases - Hydrolyses ATP
ATP. Kinases – adds phosphate
Nucleases- breaks nucleic acids

Movement
Muscle proteins :Myosin, Actin, Flagella (found in bacteria)

Cellular control
Hormones: insulin, growth hormone, sex hormones.
Receptors: gives specific ligand recognition to induce response.

Transport
Respiratory proteins. e.g. haemoglobin - oxygen carrying ,
Cytochromes – electron transport.
Storage: Ferritin- stores iron in its soluble and non-toxic form.

Structural
Skin, Bones – Collagen
Hair, Fingernails- Keratin

Immune system- (Defence against toxins/pathogens.)
Antibodies, complement system, T-cell receptors.

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3
Q

Peptide examples

(just for some extra info)

A

Oxytocin
Chain length = 9
Function:
Contracts uterus & helps lactation. Synthetic version to induce labor

Somatostatin
Chain length = 14
Function:
Inhibits the release of growth hormone. Used for ulcer treatments

Melittin
Chain length = 26
Function:
Bee Venom. Used to treat rheumatoid arthritis

Calcitonin
Chain length = 32
Function:
Regulates calcium. Used for treatment of osteoporosis

Beta amyloid
Chain length = 42
Function:
BAD one. Causes Alzheimer disease. Present in amyloid plaques in the brains.

Insulin
Chain length = 51
Function:
Control glucose levels. Used in treatment of diabetes

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4
Q

What is the function of protein dependent on?

A

The function of protein is dependent on:

-Amino acid composition & sequence (unique to protein)

Structure (size and shape)

Chemical properties of amino acids – can vary depending on 3D structure

Post translational modifications – such as phosphorylation, glycosylation

Other molecules that can bind to proteins such as cofactors, metal ions, ligands or even protein - protein interactions

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5
Q

Composition

Proteins- linear polymers of amino acids

How many different kinds of amino acids are there and how do they differ?

What does the order in which the amino acids are linked gives rise to?

A

There are 20 different kinds of amino acids each differing in R groups. (they have different R groups)

The order in which the amino acids are linked gives rise to a sequence or primary structure

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6
Q

(Name the 3 groups in an (alpha) amino acid)

A

α - Amino group (NH2)
α - Carboxylic group (COOH)
R group (20 types)

NH2 - CH(R) - COOH

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7
Q

What is unique about the α – carbon in the amino acid?

A

α – carbon is asymmetric (chiral) for 19 amino acids.
Only 1 (where R = hydrogen) is non-chiral

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8
Q

Abundant : each cell has more than 100,000 different proteins with more than 50% dry cell wt

A
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9
Q

Amino acid configuration

(Flashcard for understanding but can attempt to memorise- helpful to do so)

A

L - Form
Looking along the Hydrogen - alpha Carbon bond (the bond is facing towards us). Move your eyes clockwise and see the COOH group then the -R group then the -NH2 group. This gives the acronym CORN. The amino acid is thus L (levo).
(Look at diagram in OneNote)

D - Form

In the D (dextro) form, CORN is read only if you move your eyes anticlockwise.
(Look at diagram in OneNote)

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10
Q

L- and D- notation are same as R- and S- notation for stereo-isomers
Only the L – isomer exists naturally
The D- form is very rare and may be found in bacteria
(R- clockwise S- anticlockwise)

A
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11
Q

How is the primary sequence formed or how are amino acids linked together?

What is eliminated?

What bond is formed?

A

Formed by linking α- COOH group of one amino acid to the α-NH2 group of another.

Water is removed in this condensation reaction.

An amide bond/peptide bond is formed (CONH)
(Diagram on OneNote)

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12
Q

This reaction takes place in ribosomes as mRNA is translated into a polypeptide sequence
Amino acid sequence= Primary structure

A
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13
Q

Can continue with this….

What would three amino acids make?

A

3 amino acids would make a tripeptide

(Diagram on OneNote)

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14
Q

Tripeptide

Where is the N-terminus and C-terminus?

Which section of the molecule is an amino acid residue?

A

N- terminus (left)
(NH2 on the left)

C- terminus (right)
(Carboxyl group on the right)

Amino acid residue= ‘NHCHRCO’
Each amino acid in the sequence is a residue

When an amino acid sequences are written, the N- terminus is conventionally on the left and the C- terminus on the right
(Diagram on OneNote)

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15
Q

More and more amino acids condensed together this way builds into a polypeptide or protein sequence written from amino (N –terminus) on the left to carboxyl (C-terminus) on the right hand side.

Sequences range from few e.g. 50 to several 100 amino acids in length depending on the protein

THE 20 TYPES OF AMINO ACIDS CAN BE ARRANGED IN ANY ORDER (almost unlimited number of possible sequences)

A
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16
Q

Peptide bond Geometry

Cα= alpha carbon

Why is the –N-Cα-C- link called the peptide backbone?

A

The link –N-Cα-C- repeats throughout polypeptide sequence and so is called the peptide backbone.

17
Q

What is the length of a C-N bond and a C=N bond?

What is the actual C - N bond length for a peptide bond?

A

A single C-N bond should have a length of 1.49 Å (Angstrom).

A double C=N bond should have a bond length of 1.27 Å

The actual C-N bond length for peptide bond is 1.32 Å

(Diagram on OneNote)

18
Q

Why is the actual C-N bond length for peptide bond 1.32 Å?

Peptide bond is planar. This implies rotation is restricted, why?

A

Because the peptide bond is in resonance
Although C-N bond is shown as single bond in figures it is not able to rotate freely like a single bond. Behaves partially like a double bond (which has restricted rotation) due to resonance stabilisation.

Thus, the O—C—N—H atoms around the peptide bond lie in a single plane

The bond length is somewhere in between C-N or C=N bond lengths due to this resonance

(Diagram on OneNote)

19
Q

Where are free rotations possible?

What torsional angle does each bond rotate by?

In which direction do the favoured rotations point the R groups

A

Free rotations are possible on either side of C alpha
(Free rotation around the Cα-N bond and around Cα-C bond)

Cα-N rotates by angle phi
Cα-CO rotates by angle Psi

Favoured rotations points the R groups opposite to each other in a trans configuration (as far away from each other as possible)

(Diagram on OneNote)

20
Q

Why do nearly all amino acids prefer to be in trans conformation?

What are some exceptions?

Explain these exceptions.

A

Nearly all amino acids prefer to be in TRANS conformation to avoid steric constraint

There are some exceptions that can also be found in the CIS configuration e.g. glycine and proline

Glycine’s R group is H so it is a small molecule so it doesn’t really have steric problems
Proline has a cyclic structure - double bond character lost so rotation is possible and steric constraints not so high

21
Q

Amino acids have different side chains
20 amino acids = 20 R groups
How many R groups are: Polar, Non-polar, Acidic, Basic,
How many R groups have hydrogen bonding ?

A

Polarity: 7 are polar, 8 are non-polar
Charges: 2 are acidic, 3 are basic (out of the 7)
12 R groups can form hydrogen bonds

Proteins are thus diverse in structure and function

22
Q

Ionisation (acid-base properties)

The amino and carboxylic acid groups attached to alpha carbon can be titrated

Ionisation of weak acid:
HA ⇌ A- + H+

equation below defines the ratio of the
protonated to non-protonated (conjugate base) form.
pH = pKa + log ([A-]/[HA])
(Henderson-Hasselbalch equation)

A
23
Q

Zwitterionic character

A

For amino acids the ionisation can be written similarly with acid (protonated) form of ionisable group on the left.
e.g. glycine where R = hydrogen

α-Amino group
NH3+ ⇌ NH2 + H+
pH = pKa + log ([NH2]/[NH3+])

α- Carboxyl group
COOH ⇌ COO- + H+
pH = pKa + log ([COO-]/[COOH])

24
Q

Equations to remember

% ionised of an acid =
100 / 1 + antilog (pKa-pH)

% protonated of a base =
100 / 1 + antilog (pH-pKa)

At pH = 7.0 this gives charge of (+ 1) from amine and (-1) from carboxyl.

At pH 7, both –ve and + ve charges predominates giving Zwitterionic (net charge 0)

A
25
Q

Diagram of a graph showing an amino acid when both groups are protonated and deprotonated and when it is in the zwiterrionic form on OneNote

A
26
Q

When is a group deprotonated and when is a group protonated?

A

At a pH greater than the pKa, the group is deprotonated

At a pH less than the pKa, the group is protonated

27
Q

What is the isoelectric point of an amino acid?
Equation to work it out

A

The pH at which the amino acid has zero net charge

The isoelectric point is the average of the two pKa values for the α-carboxyl and α-amino groups

pI = (pKa 1 + pKa 2) / 2

28
Q

What charge would the amino acid or protein sequence have if the pH is greater than the isoelectric point or less than the isoelectric point?

A

For any amino acid or protein sequence :

At pH > pI net charge is -ve

At pH < pI net charge is +ve

29
Q

How do you work out the pI of an amino acid that has more than 2 ionisable side chains (more than two pKas)?

A

Identify the two relevant pKa values to use (these appear either side of zwitterion)

Average only these two values

30
Q

Working out the pI of an amino acid with three pKa values

e.g. Lysine
Consider lysine with pK1 = 2.18 , pK2 = 8.95, pKR = 10.8
pK1= COOH
pK2= NH2
pKR= CH2CH2CH2CH2NH2

A

pI = (8.95 + 10.8) / 2 = 9.88

We choose these pKa values because once the pH becomes greater than pK2 the amino acid becomes a zwitterion and once the pH becomes greater than pKR it is no longer a zwitterion- these pKa values are on either side of the zwitterion

(Diagram on One Note)

31
Q

What are the 5 classifications of amino acid side chains?

A

Aliphatic & non-polar side chains
Basic & hydrophilic side chains
Acidic & hydrophilic side chains
Aromatic side chains
Hydrophilic, but neutral side chains

32
Q

How many amino acids have aliphatic side chains? Name them.

How many chiral centres do each of these amino acids have?

What happens as the number of carbon atoms increase?

A

Five amino acids have aliphatic side chains

- Glycine - no chiral carbon
- Alanine - one chiral carbon
- Valine - one chiral carbon
- Leucine - one chiral carbon
- Isoleucine - two chiral carbons

They are more bulky, more hydrophobic and less flexible as the number of carbons increase

(Diagram of the amino acids on OneNote)

33
Q

There are two other amino acids that have both non-polar and aliphatic side chains.
Name these

A

Methionine and proline

(In proline the carbon side chain is bonded to the a-amino nitrogen to form heterocyclic ring)

(Diagram of the 2 amino acids on One Note)

34
Q

Which amino acids have basic side chains (hydrophilic)?

State what pKa each side chain has

A
  • Lysine
    • Arginine
    • Histidine

Arginine side chain has the highest Pka (~13) so is always protonated

Lysine side chain has Pka ~ 10 so is fully protonated at pH 7.0

Histidine side chain has Pka ~ 7 so ~50% ionised at physiological pH. This is useful in proton transfer e.g. enzymes

(Diagram of the 3 amino acids on OneNote)

35
Q

Which amino acids have acidic side chains (hydrophilic)?

What is the pKa of the COOH group and so what does this tell you about its ionisation state at pH 7?

A
  • Aspartate
    • Glutamate

Carboxylic acid in the side chain can donate a proton to become negative

The pKa of the COOH group is ~4. Thus, at pH 7 it would be in the CO2- form.
This is why they are most often called Aspartate & Glutamate rather than their acid forms.

(Diagram of the 2 amino acids on OneNote)

36
Q

Which amino acids have aromatic side chains?

Which amino acid is the most hydrophobic and which absorbs must in UV?

A
  • Tyrosine (note there is an acidic phenol site on tyrosine)
  • Phenylalanine
  • Tryptophan

Phe is the most hydrophobic.
It does absorb UV but weak.

Trp absorbs most in UV

(Diagram of the 3 amino acids on OneNote)

37
Q

Which amino acids are (weakly) hydrophilic but neutral?

A

Serine (R = CH2OH )

Threonine (R = CH(OH)CH3)

Cysteine (R = CH2SH)

Asparagine (Asn) (R = CH2CONH2)

Glutamine (Gln) (R = CH2CH2CONH2)

38
Q

Ionisable side chains
Glu, Asp usually have a negative charge
Lys usually has a positive charge
Arg always has a positive charge

pKa values in proteins are sometimes hugely altered by environment of active site

If you have two cysteine’s nearby each other they can form disulfide bonds (with the SH groups)

Insulin has these disulphide bonds

A

MPHARM (13 decks)

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